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- PDB-2kjh: NMR based structural model of the UBCH8-UBIQUITIN complex -

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Basic information

Entry
Database: PDB / ID: 2kjh
TitleNMR based structural model of the UBCH8-UBIQUITIN complex
Components
  • Ubiquitin/ISG15-conjugating enzyme E2 L6
  • Ubiquitin
KeywordsLigase/protein binding / Protein-protein interaction / HADDOCK model / E2 enzyme / ATP-binding / Ligase / Nucleotide-binding / Ubl conjugation pathway / Cytoplasm / Isopeptide bond / Nucleus / Ubl conjugation / Ligase-protein binding COMPLEX
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / : / : / protein modification process => GO:0036211 / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...ISG15 transferase activity / ISG15-protein conjugation / : / : / protein modification process => GO:0036211 / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of BACH1 activity / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Degradation of DVL / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin/ISG15-conjugating enzyme E2 L6 / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the mean structure, model 1
AuthorsSerniwka, S.A. / Shaw, G.S.
CitationJournal: Biochemistry / Year: 2009
Title: The structure of the UbcH8-ubiquitin complex shows a unique ubiquitin interaction site.
Authors: Serniwka, S.A. / Shaw, G.S.
History
DepositionMay 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin/ISG15-conjugating enzyme E2 L6
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)26,2822
Polymers26,2822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 200Structures with the lowest energy in the lowest energy cluster
RepresentativeModel #1closest to the mean structure

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Components

#1: Protein Ubiquitin/ISG15-conjugating enzyme E2 L6 / Ubiquitin-protein ligase L6 / Ubiquitin carrier protein L6 / UbcH8 / Retinoic acid-induced gene B ...Ubiquitin-protein ligase L6 / Ubiquitin carrier protein L6 / UbcH8 / Retinoic acid-induced gene B protein / RIG-B


Mass: 17659.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L6, UBCH8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14933, ubiquitin-protein ligase
#2: Protein Ubiquitin /


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A UBA80, UBCEP1, UBA52, UBB, UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62988, UniProt: P0CG48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: THESE MODELS WERE DETERMINED FROM DOCKING OF UBCH8 AND UBIQUITIN BASED ON CHEMICAL SHIFT PERTURBATION AND SATURATION TRANSFER EXPERIMENTS. AS THE STARTING STRUCTURES WERE X-RAY COORDINATES, ...Details: THESE MODELS WERE DETERMINED FROM DOCKING OF UBCH8 AND UBIQUITIN BASED ON CHEMICAL SHIFT PERTURBATION AND SATURATION TRANSFER EXPERIMENTS. AS THE STARTING STRUCTURES WERE X-RAY COORDINATES, NO SIDE CHAIN PROTONS ARE INCLUDED IN THE FINAL STRUCTURE FILE.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1422D 1H-15N HSQC
1523D HN(CA)CB
1623D CBCA(CO)NH
1732D 1H-15N HSQC with Cross Saturation
1842D 1H-15N HSQC with Cross Saturation

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7, 90% H2O/10% D2O90% H2O/10% D2O
20.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14, 90% H2O/10% D2O90% H2O/10% D2O
30.35 mM [U-100% 15N; U-99% 2H] UbcH8-15, 0.35 mM Ubiquitin-16, 20 mM sodium phosphate-17, 1 mM EDTA-18, 250 mM sodium chloride-19, 50 mM Arginine-20, 50 mM Glutamic Acid-21, 90% H2O/10% D2O90% H2O/10% D2O
40.35 mM UbcH8-22, 0.35 mM [U-100% 15N; U-99% 2H] Ubiquitin-23, 20 mM sodium phosphate-24, 1 mM EDTA-25, 250 mM sodium chloride-26, 50 mM Arginine-27, 50 mM Glutamic Acid-28, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMUbcH8-1[U-100% 13C; U-100% 15N]1
0.35 mMUbiquitin-21
20 mMsodium phosphate-31
1 mMEDTA-41
250 mMsodium chloride-51
50 mMArginine-61
50 mMGlutamic Acid-71
0.35 mMUbcH8-82
0.35 mMUbiquitin-9[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-102
1 mMEDTA-112
250 mMsodium chloride-122
50 mMArginine-132
50 mMGlutamic Acid-142
0.35 mMUbcH8-15[U-100% 15N; U-99% 2H]3
0.35 mMUbiquitin-163
20 mMsodium phosphate-173
1 mMEDTA-183
250 mMsodium chloride-193
50 mMArginine-203
50 mMGlutamic Acid-213
0.35 mMUbcH8-224
0.35 mMUbiquitin-23[U-100% 15N; U-99% 2H]4
20 mMsodium phosphate-244
1 mMEDTA-254
250 mMsodium chloride-264
50 mMArginine-274
50 mMGlutamic Acid-284
Sample conditionsIonic strength: 250 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1Variancollection
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
NMRView5.2.2Johnson, One Moon Scientificdata analysis
HADDOCK2Dominguez, Boelens, Bonvinrefinement
HADDOCK2Dominguez, Boelens, Bonvinstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Semi-rigid body docking using previously determined structures of UbcH8 and ubiquitin; calculated 1000 structures-200 low energy structures selected, Semi-flexible simulated annealing and ...Details: Semi-rigid body docking using previously determined structures of UbcH8 and ubiquitin; calculated 1000 structures-200 low energy structures selected, Semi-flexible simulated annealing and refinement with explicit water
NMR representativeSelection criteria: closest to the mean structure
NMR ensembleConformer selection criteria: Structures with the lowest energy in the lowest energy cluster
Conformers calculated total number: 200 / Conformers submitted total number: 16

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